Protein Folding And Function

Question 1

Secondary structure

Answer 1

Local spatial arrangement (folding) of the polypeptide backbone (not the R groups)

H-bonds

Question 2

Tertiary structure

Answer 2

3D arrangement of all atoms in a polypeptide

Covalent (disulphide), ionic, H-bonds, VdW, hydrophobic

Question 3

Primary structure

Answer 3

The linear amino acid sequence of the polypeptide chain

Covalent peptide bonds

Question 4

Quaternary structure

Answer 4

3D arrangement of protein subunits (more than one polypeptide chain)

Covalent (disulphide), ionic, H-bonds, VdW, hydrophobic

Question 5

Alpha helix

Answer 5

3.6aa per turn
0.54nm pitch
Right Handed Helix
0.15nm between residues
(side chains are not involved in the folding)
Ala and Leu are helix formers
Pro and Gly are helix breakers

Question 6

Beta strand

Answer 6

0.35nm between aa residues
R groups alternate between opposite sides of the chain
Can form antiparallel beta sheets (bonds at less of an angle than the parallel beta sheets)

Question 7

Fibrous proteins

Answer 7

Role - support, shape and protection
Long strands or sheets
Single type of repeating secondary structure
e.g. Collagen

Question 8

Globular proteins

Answer 8

Role - catalysis and regulation
Compact shape
Involves several types of secondary structure
e.g. Haemoglobin and all enzymes

Motifs - folding patterns containing 1 or more elements of secondary structure
Domains - part of pp that folds into a distinct chain - often has a specific role

Question 9

Collagen

Answer 9

Triple helical arrangement of collagen chains
Gly-X-Y repeating sequence
H-bonds stabilise chains
Collagen fibrils - covalently cross-linked collagen molecules (10x stronger than steel)

Question 10

Water soluble proteins

Answer 10

Polypeptide chains fold so that hydrophobic side chains are buried and polar, charged side chains are on the surface

Question 11

Haemoglobin

Answer 11

2 alpha and 2 beta subunits
held together by non- covalent interactions
1 subunit can bind to 1 molecule of O2

Question 12

Disulphide bonds

Answer 12

Formed between Cys residues
Can be broken with reducing agents
Most proteins with disulphide bonds are secreted e.g. ribonuclease

Question 13

Electrostatic Attractions

Answer 13

Formed between charged groups
Glu-, Asp- and Arg+, Lys+, His+
‘Salt Bridge’

Question 14

Hydrogen bonds

Answer 14

Formed between an electronegative atom and a hydrogen bound to another electronegative atom

Question 15

Hydrophobic effect

Answer 15

Interaction between hydrophobic side chains to exclude water

Question 16

Van der Waals forces

Answer 16

Dipole-dipole interactions

Important when surfaces of 2 large molecules come together

Question 17

Protein denaturing

Answer 17

Loss of overall shape cause by breaking bonds
Increase in heat and a change of pH
Detergents/organic solvents

Question 18

Protein folding

Answer 18

All the information about folding is contained in the primary sequence - not random
Some proteins require chaperones to assist in folding - stops mis-folding

Question 19

Mis-folding and disease

Answer 19

Transmissible spongiform encephalopathies

- abnormally shaped proteins clump together - happens in Alzheimer’s - causes amyloidoses

Question 20

Amyloid fibres

Answer 20

Mis-folded insoluble form of a normally soluble protein

Do not break down, take a long time to form - late onset - ultimately causes the disease